His international team mate Cedric Bakambu, who plays for Spanish club Villarreal, was booked on the same plane and reached Kinshasa the next day on a different flight.
Congolese Football Federation (CFF) president Constant Omari told French radio on Monday that Mbokani faced possible sanctions for missing the games.
Mbokani, who is on loan at the Premier League club from Dynamo Kiev, told Congolese radio on Wednesday he had decided to stop playing for his country.
"I do not want to play for Congo," he said. "I find the treatment unfair. Therefore, after discussion with my family, my relatives, I decided to stop.
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Omari said that Mbokani had not informed the CFF of his decision.
"He hasn't been in touch directly with the CFF...," Omari was quoted as saying by Sky Sports.
"It's not for Mbokani to quit international football. You can't just get up in the morning and decide you're not playing for your country anymore. It's up to the national selectors if they want to pick him."
(Reporting by Simon Jennings in Bengaluru; editing by John Stonestreet)
